Systemic immune responses are regulated by diverse host and pathogen effectors and variation in innate and inflammatory immunity mediate downstream effects on adaptive immune responses. Not surprisingly, a significant range in inter-individual immune responses is noted In humans and mammals, especially in the respiratory tract where virus-immune interactions can be protective or pathogenic. We will identify polygenic immune traits which mediate unique and conserved immune responses, testing the hypothesis that the most significant, highly conserved immune pathways will best be identified in genetically diverse populations that model naturally occurring variation. Thus, we employ the Collaborative Cross (CC), a highly diverse, infinitely reproducible, and customizable recombinant inbred (Rl) mouse panel designed to discover polygenic traits that regulate complex phenotypes, like immunity. The CC captures: a) vast host genetic diversity, b) extreme immune phenotypes, and c) polygenic trait regulation of host immune responses to infection. In Project 1, we use the highly tractable SARS-Coronavirus (SARS-CoV) model to probe immune function in the lung. In the CC, SARS-CoV infection manifests in protective or pathogenic immune phenotypes including diffuse alveolar damage, atypical pneumonia, and acute respiratory distress. Importantly, the SARS-CoV model Is supported by: a) robust genetic, biochemical, immunologic, and virologic tools, b) host immune regulated pathogenic outcomes, c) polygenic traits regulating immune pathways, d) virulence genes which modulate immunity, and e) defined components of protective immunity and clearance. In Aim 1, we will identify genes and expression networks that regulate the kinetics, composition, and magnitude of innate immunity and inflammation in the lung. In Aim 2, we identify genes and polygenic networks that regulate the kinetics, magnitude, and effector functions of SARS-CoV specific CDS T cells or the kinetics, avidity, and functional breadth of SARS-CoV specific antibody responses. In aim 3, we validate the role of genes and polymorphic interactions in unique and conserved immune responses, in immune cross talk, in protective or pathologic disease, and across organs, viruses and host species.